changing position of atoms during NAMD simulation

From: michael_at_perfect-kreim.de
Date: Mon Jan 14 2008 - 07:11:52 CST

Hi all,

for my diploma-thesis I need a system to change the position of atoms
during simulation.
What I am planing to do is:
I have a water-box with ions and every time an ion crosses a given
z-coordinate the ion should be moved back to its "site" of the box.
I cannot work with forces or constrains, because I need the number of
atoms that cross the z-coordinate and I need fixed concentrations.
So I have to reset the coordinate of the ion.

My main question is:
Is it possible with NAMD (and VMD or another program) to change the
coordinates of atoms during simulation if the coordinates exceed a given
value?

I tried to enter some TCL-code in my NAMD-config-file, but this code is
only executed once and not every timestep.

Then I found this "Interactive Molecular Dynamics Simulation"-thing but
as far as I understand it, it can only apply forces.

Maybe there is a possibility to write some plugin for NAMD?
I am open to anything.

Thanks a lot for your answer.

Best regards,

Michael

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:11 CST